Journal of Engineering Education Transformations

Open Access Open Access  Restricted Access Subscription Access
Open Access Open Access Open Access  Restricted Access Restricted Access Subscription Access

In Silico Based Bioinformatics Project during the COVID-19 Lockdown Period : An Alternative to Wet Lab Study


Affiliations
1 Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
     

   Subscribe/Renew Journal


In the weeks and months following the COVID outbreak, millions of students around the world are forced to switch over from traditional classroom learning to online learning. This unprecedented move had tremendous impact on the mode of learning project based courses. In particular, the field of biological science project based courses which require the students and faculty to work in the laboratory was impacted. 5 students and a faculty from Kalasalingam Academy of Research and Education used modern in silico tools, databases and software to study a biological problem related to antibiotic resistance in a bacterium called Enterobacter hormaechei subsp. hoffmannii OIPH-N069. The students used freely available modern bioinformatics tools, databases and software such as NCBI, PROTPARAM, SOPMA, BLAST, CLUSTAL OMEGA, CDD, SWISS-MODEL server, PATCHDOCK, PYMOL and CARD to carry out the research work. This method of doing the project has resulted in the phase I completion of the project course successfully. This methodology of usage of freely available tools, databases and software will help students worldwide to pursue the project based biology courses successfully. The significance of this study is the capability of students in completion of the biology project with the usage of only computer and internet and not to depend upon expensive wet lab study.

Keywords

Bioinformatics, In Silico, Project, Computer, COVID.
Subscription Login to verify subscription
User
Notifications
Font Size


  • Sambrook, J. and Russell, D. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

  • Rajnish, K.N., Kishore Choudhary G.M., and Gunasekaran P. (2008). Functional characterization of a putative endoglucanase gene in the genome of Zymomonas mobilis. Biotechnology letters. 30,1461- 1467.

  • Liang, W.L., Huang, H.M., Lin R.D., and Hou, W.C. (2003). Screening for natural inhibitors of penicillinase by copolymerization of hydrolyzed sodium dodecyl sulphate polyacrylamide gels for detecting penicillinase activity. Bot. Bull. Acad. Sin. 44,187-191.

  • [IV]. Wong, A., Vohra, R., Kopec, K., Brooke, N., and Stolbach, A. (2020). The Importance of Continuing Medical Education During the COVID-19 Pandemic: the Global Educational Toxicology Uniting Project (GETUP). Journal of Medical Toxicology, 16, 340- 341.

  • [V]. Peters, M. A., Rizvi, F., McCulloch, G., Gibbs, P., Gorur, R., Hong, M., and Misiaszek, L. (2020). Reimagining the new pedagogical possibilities for universities post-Covid-19: An EPAT Collective Project. Educational Philosophy and Theory, 1-44.

  • [VI] Yustina, Y., Syafii, W., and Vebrianto, R. (2020). The Effects of Blended Learning and Project-Based Learning on Pre-Service Biology Teachers’ Creative Thinking Skills through Online Learning in the Covid- 19 Pandemic. Jurnal Pendidikan IPA Indonesia, 9(3), 408-420.

  • [VII] Murphy, M. P. (2020). COVID-19 and emergency eLearning: Consequences of the securitization of higher education for post-pandemic pedagogy. Contemporary Security Policy, 41(3), 492-505.

  • [VIII] Bao, W. (2020). COVID‐ 19 and online teaching in higher education: A case study of Peking University. Human Behavior and Emerging Technologies, 2(2), 113-115.

  • [IX]. Zayapragassarazan, Z. (2020). COVID-19:Strategies for Engaging Remote Learners in Medical Education. Online Submission, 9(273), 1-18.

  • [X]. Sahu, P. (2020). Closure of universities due to coronavirus disease 2019 (COVID-19): impact on education and mental health of students and academic staff. Cureus, 12(4).

  • [XI]. Zhao, Y. (2020). COVID-19 as a catalyst for educational change. Prospects, 49(1), 29-33.

  • [XII]. Wijesooriya, N. R., Mishra, V., Brand, P. L., and Rubin, B. K. (2020). COVID-19 and telehealth, education, and research adaptations. Paediatric Respiratory Reviews.

  • [XIII]. Jena, P. K. (2020). Impact of Covid-19 on higher education in India. International Journal of Advanced Education and Research (IJAER), 5.

  • [XIV]. Seo, J.S., Chong, H., Park, H.S., Yoon, K.O., Jung, C., Kim, J.J., Hong, J.H., Kim, H., Kim, J.H., Kil, J.I., Park, C.J., Oh, H.M., Lee, J.S., Jin, S.J., Um, H.W., Lee, H.J., Oh, S.J., Kim, J.Y., Kang, H.L., Lee, S.Y., Lee, K.J. and Kang, HS. 2005. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol. 23: 63-68.

  • [XV]. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server, pp. 571-607. In: Walker, J.M. (ed.), The Proteomics Protocols Handbook, Humana Press, New York.

  • [XVI]. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.

  • [XVII]. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.

  • [XVIII]. Marchler-Bauer, A., Anderson, J.B., Cherukuri, P.F., DeWeeseScott, C., Geer L.Y., Gwadz, M., He, S., Hurwitz, D.I., Jackson, J.D., Ke, Z., Lanczycki, C.J., Liebert, C.A., Liu, C., Lu F., Marchler, G.H., Mullokandov, M., Shoemaker, B.A., Simonyan, V., Song, J.S., Thiessen, P.A., Yamashita, R.A., Yin, J.J., Zhang, D. and Bryant, S.H. (2005). CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res. 33: 192-196.

  • [XIX]. Schwede, T., Kopp, J., Guex, N.. and Peitsch, M.C. (2003). SWISSMODEL: an automated protein homology-modelling server. Nucleic Acids Res. 31: 3381-3385.

  • [XX]. DeLano, WL. The PyMOL Molecular Graphics System. http:// www.pymol.org.

  • [XXI] Shenoy, V., Mahendra, S., and Vijay, N. (2020). COVID 19 lockdown technology adaption, teaching, learning, students engagement and faculty experience. Mukt Shabd Journal, 9(4), 698-702.

  • [XXII] Calder, A., Sole, G., and Mani, R. (2020). Physiotherapy student research projects during the COVID19 lockdown. Physical Therapy Reviews, 1-2.

  • [XXIII] Mishra, L., Gupta, T., and Shree, A. (2020). Online teaching-learning in higher education during lockdown period of COVID-19 pandemic. International Journal of Educational Research Open, 1, 100012.

  • [XXIV] Raaen, K., Sørum, H., and Gonzalez, R. (2020, November). IT bachelor capstone project during lockdown: Student experiences. In Norsk IKT-konferanse for forskning og utdanning, (No. 4).

  • [XXV] K.S. Mohammed, Rashid, C. A., Salih, H. A., and Budur, T. (2020). The role of online teaching tools on the perception of the students during the lockdown of Covid-19. International Journal of Social Sciences and Educational Studies, 7(3), 178.

  • [XXVI] Van Haeften, S., Milic, A., Addison‐Smith, B., Butcher, C., Davies, J. M. (2020). Grass Gazers: Using citizen science as a tool to facilitate practical and online science learning for secondary school students during the COVID‐19 lockdown. Ecology and evolution.


Abstract Views: 189

PDF Views: 1




  • In Silico Based Bioinformatics Project during the COVID-19 Lockdown Period : An Alternative to Wet Lab Study

Abstract Views: 189  |  PDF Views: 1

Authors

S. Sheik Asraf
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
A. Sivakkanni
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
M. Sneha
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
S. Janani
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
P. Jashin
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India
A. Martina Jemimal
Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil-626 126, India

Abstract


In the weeks and months following the COVID outbreak, millions of students around the world are forced to switch over from traditional classroom learning to online learning. This unprecedented move had tremendous impact on the mode of learning project based courses. In particular, the field of biological science project based courses which require the students and faculty to work in the laboratory was impacted. 5 students and a faculty from Kalasalingam Academy of Research and Education used modern in silico tools, databases and software to study a biological problem related to antibiotic resistance in a bacterium called Enterobacter hormaechei subsp. hoffmannii OIPH-N069. The students used freely available modern bioinformatics tools, databases and software such as NCBI, PROTPARAM, SOPMA, BLAST, CLUSTAL OMEGA, CDD, SWISS-MODEL server, PATCHDOCK, PYMOL and CARD to carry out the research work. This method of doing the project has resulted in the phase I completion of the project course successfully. This methodology of usage of freely available tools, databases and software will help students worldwide to pursue the project based biology courses successfully. The significance of this study is the capability of students in completion of the biology project with the usage of only computer and internet and not to depend upon expensive wet lab study.

Keywords


Bioinformatics, In Silico, Project, Computer, COVID.

References





DOI: https://doi.org/10.16920/jeet%2F2022%2Fv35i3%2F22090